Are both of the amplifier's input level controls set to the same level?
Yes, they are. Both at full.
Are the speaker leads connected to the Ch1+ and the CH2+ of the amplifier's banana jacks?
Both are going into the positive. The central two jacks.
What is the power rating of your speakers?
The speakers are Avatars. One, a 410NEO, is rated at 1000W. The other, a 115Delta is 500. I know the Delta's power rating is approaching the limit. But I wasnt pushing it very hard at all when the problem was occuring. The pre was only running at half volume and half gain (12 o'clock). The strange thing was the lack of volume. Both speakers were going much louder with the previous amp (Only 400W) with no distortion or break up.